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// List of things that still need doing
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// Likelihood calculations
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1.)  Need to examine time spent messing about with probabilities with multiple processes
2.) Need to make some fast rate 0 calculations
3.) Need an intelligent way of specifying the rate of processes (particularly when using covarion models)


// User feedback

1. Currently get "buggered" when running on AA data with a DNA model. Need more graceful leave. (Julie Huxley-Jones)
2. Currently fails when only two species in the analysis. (Tim Massingham)
3. Doesn't deal with ambiguity charactors -- returns unhelpful message "tried to return unknown type". (Tim Massingham)
4. Get "buggered" with stepwise addition -- 4 species tree with 1734 nucleotides. (Tim Massingham)


// People's suggested ideas

1. RY model. A 2-state model for analysing (e.g.) pyrimidine and purine changes
2. Comparison of expected site patterns compared to those observed in the data. Do they seem reasonable?
3. Combining DNA and amino acid data. Why can't the likelihood for both contribute to tree estimation?
4. Why not make prep available for people to use?
5. Partitioning data is going to become important.

// Ideas I've had










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